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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:NAT1-PCM1 (FusionGDB2 ID:57312)

Fusion Gene Summary for NAT1-PCM1

check button Fusion gene summary
Fusion gene informationFusion gene name: NAT1-PCM1
Fusion gene ID: 57312
HgeneTgene
Gene symbol

NAT1

PCM1

Gene ID

10991

5108

Gene namesolute carrier family 38 member 3pericentriolar material 1
SynonymsG17|NAT1|SN1|SNAT3PTC4|RET/PCM-1
Cytomap

3p21.31

8p22

Type of geneprotein-codingprotein-coding
Descriptionsodium-coupled neutral amino acid transporter 3N-system amino acid transporter 1Na(+)-coupled neutral amino acid transporter 3system N amino acid transporter 1system N1 Na+ and H+-coupled glutamine transporterpericentriolar material 1 proteinPCM-1hPCM-1pericentriolar material 1, PCM1
Modification date2020031320200327
UniProtAcc

P18440

Q15154

Ensembl transtripts involved in fusion geneENST00000307719, ENST00000518029, 
ENST00000539092, ENST00000541942, 
ENST00000545197, ENST00000517441, 
ENST00000517492, ENST00000520546, 
ENST00000535084, 		ENST00000325083, 
ENST00000519253, ENST00000524226, 
ENST00000327578, ENST00000518537, 
ENST00000518936, 
Fusion gene scores* DoF score4 X 4 X 3=4810 X 14 X 6=840
# samples 413
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/840*10)=-2.69187770463767
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NAT1 [Title/Abstract] AND PCM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPCM1(17843596)-NAT1(18028188), # samples:2
NAT1(18067689)-PCM1(17882870), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneNAT1

GO:0006867

asparagine transport

10823827

HgeneNAT1

GO:0006868

glutamine transport

10823827

HgeneNAT1

GO:0015808

L-alanine transport

10823827

HgeneNAT1

GO:0015817

histidine transport

10823827


check buttonFusion gene breakpoints across NAT1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across PCM1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4BRCATCGA-D8-A1XY-01ANAT1chr8

18067689

+PCM1chr8

17882870

+


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Fusion Gene ORF analysis for NAT1-PCM1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5UTR-3CDSENST00000307719ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000307719ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000307719ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000518029ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000518029ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000518029ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000539092ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000539092ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000539092ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000541942ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000541942ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000541942ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000545197ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000545197ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-3CDSENST00000545197ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000307719ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000307719ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000307719ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000518029ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000518029ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000518029ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000539092ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000539092ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000539092ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000541942ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000541942ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000541942ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000545197ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000545197ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
5UTR-intronENST00000545197ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000517441ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000517441ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000517441ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000517492ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000517492ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000517492ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000520546ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000520546ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000520546ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000535084ENST00000325083NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000535084ENST00000519253NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-3CDSENST00000535084ENST00000524226NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000517441ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000517441ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000517441ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000517492ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000517492ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000517492ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000520546ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000520546ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000520546ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000535084ENST00000327578NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000535084ENST00000518537NAT1chr8

18067689

+PCM1chr8

17882870

+
intron-intronENST00000535084ENST00000518936NAT1chr8

18067689

+PCM1chr8

17882870

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for NAT1-PCM1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
NAT1chr818067689+PCM1chr817882869+0.736351430.2636486
NAT1chr818067689+PCM1chr817882869+0.736351430.2636486

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for NAT1-PCM1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:17843596/:18028188)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
NAT1

P18440

PCM1

Q15154

FUNCTION: Participates in the detoxification of a plethora of hydrazine and arylamine drugs. Catalyzes the N- or O-acetylation of various arylamine and heterocyclic amine substrates and is able to bioactivate several known carcinogens.FUNCTION: Required for centrosome assembly and function (PubMed:12403812, PubMed:15659651, PubMed:16943179). Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2 (PubMed:12403812, PubMed:15659651). Required to anchor microtubules to the centrosome (PubMed:12403812, PubMed:15659651). Also involved in cilium biogenesis by recruiting the BBSome, a ciliary protein complex involved in cilium biogenesis, to the centriolar satellites (PubMed:20551181, PubMed:24121310, PubMed:27979967). {ECO:0000269|PubMed:12403812, ECO:0000269|PubMed:15659651, ECO:0000269|PubMed:16943179, ECO:0000269|PubMed:20551181, ECO:0000269|PubMed:24121310, ECO:0000269|PubMed:27979967}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for NAT1-PCM1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for NAT1-PCM1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for NAT1-PCM1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for NAT1-PCM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource